The Botanist
by ShannaA1
Summary: Begins after Missing. John/OFC friendship.
1. Insults and Insomnia

_Disclaimer: If you recognize it, it doesn't belong to me. _

_Takes place in season four after Missing._

* * *

Lily Avery had never been more than two states away from her family's peaceful home in Georgia at any time in her life, unless one counted the two months she'd spent at the SGC (and she didn't).

And suddenly, she'd been sent to the towering city of Atlantis – she still wasn't sure why they needed another botanist, but didn't say that out loud. These people…they all laughed, lived, worked together – two hundred of them.

_You can do this_, she thought – over and over throughout that first day, and for a week afterward. Eventually she started to believe it.

That is, until she collided with Rodney McKay one afternoon as she was leaving the botany lab. The tablet he'd been clutching slipped from his grasp; she barely managed to catch it before it hit the floor, and handed it back to him.

"Valuable research, here! Why don't you watch where you're going?!" If she'd been anyone other than the strong Southern girl her mother had raised her to be, she might have burst into tears at the angry tone.

As it was, she snapped back, "If you'd follow your own advice, this wouldn't have happened!" Her accent grew more pronounced when she was irritated, and she mentally kicked herself for turning 'advice' into 'ad-vais.'

He scowled at her for a moment before his com beeped. Another moment passed before he replied shortly, "Had a run-in with Scarlett O'Hara. I'll be right there."

McKay – for that was who he had to be, as he fit the description she'd heard on board the Daedalus – hurried off.

--

A month passed, then two, in which Lily endured many teasing remarks – in and out of the botany lab. No one seemed to want to let her forget how amusing they thought it was that she was a botanist named for a flower. She let them have their fun, though, and laughed along with them.

They didn't know she suffered from insomnia, didn't know she walked the city at night until she could barely hold her head up, didn't know she cried with every step. It wasn't because of them – the friendly teasing she could take – but because, even now, she missed her sisters terribly.

One particular night, sleep just wasn't coming. Usually it took only an hour before weariness overtook her, but tonight she'd been walking for more than two. Before long, she found herself on a balcony staring out at the water.

She didn't remember falling asleep, but judging by the shoe repeatedly prodding her hard in the side, she'd been dead to the world.

"Quit that," she grumbled, opening her eyes a fraction. For a moment, things were foggy; then, suddenly, John Sheppard slid into focus above her. She was grateful he'd found her, and not someone else; he was a friend already, which was entirely due to their shared taste in music. Hell, that was how he'd ever even learned her name – on her first evening in the city, he'd caught her singing "Folsom Prison Blues" on a different balcony.

"Do you always sleep out here, or is this just a one-time thing?"

"Help me up, get me some coffee, and I'll tell you." He held out a hand, pulled her to her feet. Before too long, a cup of steaming coffee with sugar was in her hands and she was telling John exactly why he'd found her where he had.

"You could've just gone to see Keller. She'd give you Ambien or something."

"I've always walked the halls at night, Colonel. _Always_. Never believed in taking sleeping pills."

"Whatever floats your boat, Avery. Just do me a favor and don't make a habit of sleeping outside."

She grinned in reply, and was about to ask what time it was – before remembering that it was her day off anyway. No need to rush to the botany lab.

"Well," Sheppard said after a few minutes of easy silence. "I should go, got a mission to get ready for."

"Be careful, won't you?"

"I'm offended that you think I'd ever be anything else."

"Get along with you, trouble magnet! I'll see you when you get back."

"We'll be back in time for dinner," he predicted, getting up to leave. Lily just went back to her coffee with a sigh, knowing as well as he did that it would likely turn out to be wishful thinking.

* * *

**A/N**: This whole thing came about due to a dream I had in which McKay called someone Scarlett O'Hara. And lo, Lily was born roughly ten hours later after I thought way too much about the aforementioned dream.


	2. The Truth About Women

_Disclaimer: Nothing's mine but Lily._

_Tag to BAMSR._

* * *

She found him on a balcony, losing golf balls to the ocean. Lowering herself carefully to the ground, she waited silently behind him – as far as she knew, he didn't know she was there. That is, until he spoke.

"Should have known you'd find me."

"You're an idiot," she said, as casually as though they were discussing McKay's latest rant. He turned toward her.

"You've talked to Teyla." It wasn't a question. Lily nodded, tapped her fingers against her knee.

"I really don't think you get to be angry with her, Colonel. She made a choice."

"And you don't get to dispense your wisdom."

"Actually, I think I do. You know nothing about women, John. When it comes to protecting ourselves and our young, there's not a thing in the universe that can go up against us and win. Not the Wraith and certainly not our friends."

"That doesn't change the fact that she kept it a secret for two months, endangered its health…"

"She took a necessary risk to help defeat an enemy, so that the world her baby comes into may be a little safer in the end."

"You talk like a damn soldier. What the hell do you know about war?!"

"Three of my cousins went to Iraq, Sheppard. Two of them are dead. Don't ever imply that I don't understand _that_." She didn't recall getting up, but suddenly she was standing beside him, tears running down her face.

An obviously uncomfortable Sheppard tried the typically-male way of calming an upset woman: "Uh…please don't cry?" This method rarely worked, particularly on the dying breed of Southern ladies who relished every opportunity for a good cry.

Lily was one of them. She rested her arms on the balcony rail, and her head on her arms, and sobbed. After a moment, the lieutenant colonel quietly left.

* * *

**A/N:** Yeah, I know it's really short. I got a touch of writer's block. I'm not particularly fond of this chapter for several reasons. Let me know what y'all think.


	3. Becoming Her Mother

_Disclaimer: Again, nothing's mine but Lily.  
__Tag to Quarantine._

* * *

Lily was amazed that she hadn't lost her mind. She'd been trapped for several long hours with a Marine who had apparently been waiting a very long time for someone willing to listen to him talk.

It wasn't his fault, really; _she_ had been the one to initiate conversation, had asked where he was from. Right up until the alarms began to blare, he enthusiastically explained to her exactly why San Diego was the best place in the world.

Later on, when normalcy was restored, she learned of Sheppard's daring escape and resisted the urge to smack him.

"You are the biggest _idiot _I have ever known. What if you had _fallen_? Heaven won't take daredevils, Sheppard!"

"But I didn't!"

"You might have, and _then_ where would you – Oh, my God! I've turned into my mother!" As amusing as it probably was for the various people scattered about to hear her tirade, she had to stop there; morphing into a younger version of her mother was her biggest fear, and it had just come true.

Sheppard just giggled a little, entirely unaffected. Lily frowned at him, and stalked off. Maybe she'd go find that Marine, Sergeant – what was his name, Lassiter? – and ask him more about San Diego. He was kind of cute, and she hadn't dated since college; she would be entirely within her rights to ask if he wanted to eat lunch with her sometime.

--

And so, she did – the very next day. Quite unlike during the quarantine error, he was the one to ask questions and listened politely to her go on about her family and pets and hometown. By the time she was done, they'd been sitting in the mess hall for nearly two hours.

By dinner that night, everyone had become convinced that James Lassiter and Lily Avery were together. She was pretty sure she'd seen people making bets.

"We had lunch earlier, that's _all_!" she said to Jennifer for what seemed to be the thousandth time, pointing her fork at the pretty CMO. "Now will you give it a rest already and – what about _you_? Weren't you saying something about Ronon?"

The other woman blushed. "Wemight have almost kissed."

"Jennifer Keller, you are a horrible person! Badgering me about my Marine…and _you_ nearly kissed the most attractive fellow on base."

"_Your_Marine? I thought you just had one lunch with him," Sheppard commented from right behind her. Lily jumped; she hadn't realized he was there.

"Don't _do _that! Give me a heart attack, why don't you? I've already gotten gray hairs just from _hearing_ about your stunt yesterday, and then you go and sneak up on me!"

They just laughed at her. Lily cringed: that comment made it two times in as many days that she'd sounded far too similar to her mother.

_It can't be that bad. Mama's a perfectly lovely woman, and you should _always _aspire to be more like her,_ a little voice in the back of her head told her.

* * *

**A/N:** Another short one. Sgt. Lassiter just came out of nowhere. He'll get to show up again. Y'all might even meet Lily's mother eventually – who knows?


	4. From Home

_Disclaimer: Do I really need to say it at this point?_

* * *

The day the package arrived, Lily was barely able to get out of bed. She had spent the last two days carrying around a box of Kleenex and trying very hard not to breathe on anyone. Now she had a headache to go with that.

Jennifer brought her a mysterious, misshapen present – it was postmarked Georgia, and covered in too-bright wrapping paper that made Lily's head hurt even worse. As soon as her friend left, the sick botanist tore into the letter that accompanied it; it turned out to be from her oldest sister, Sarah-Lynn.

_Dear Lily,_

_I hope this finds you well, if at all; I wish I knew where you were. Sorry about the paper; Abigail picked it out. _

_I sent along several photos – they're already framed. Mama said to tell you that if you didn't show up at Maggie's wedding there'd be hell to pay. Don't roll your eyes at the letter, Lily Bell; I know you attended both of her previous weddings and that those marriages ended in tears, but Maggie thinks this is the one. Third time's the charm, and all. Please try and make time to come…she says she won't be able to walk down the aisle if you're not there._

_You remember Dad's old collie Tommy? Of course you do…he used to guard your door at night, and walked around the house with you when you couldn't sleep. He passed away over the summer, with that dumb old stuffed kitten that used to be yours. _

_He always did love you best._

_All my love,_

_Sarah-Lynn_

Lily sobbed bitterly, forgetting, for a few minutes, her gift. Then, picking it up, she pulled carelessly at the tape that secured the wrapping paper. Several photographs, already framed like Sarah-Lynn had said, peeked out at her.

There were three photos of Tommy in his youth – in the first, his leash flapped behind him as he ran away, grinning, from an outraged Mr. Avery; Lily had taken that photo herself, fifteen years earlier. In the second, he lay asleep, stretched out in the sunshine. In the third, he stared (with seeming incredulity) at Lily's eight-year-old self as she stood in the kitchen wearing a large sunhat, one of her mama's silk nightgowns and a pair of high heels. The last thing in the package, though, was obviously what Sarah-Lynn had been referring to.

It was a colored-pencil drawing of a brunette stick-figure surrounded by daisies and sunflowers (at least, that was what Lily _thought_ those were), titled "My Aunt Lily" in the not-quite-stable handwriting of a six-year-old. Signed 'Abby Harrison' in the same writing and decorated in one corner by a "SUPER!" sticker, doubtless courtesy of Abby's teacher, it brought happier tears to Lily's eyes.

That one was getting a place of honor on her desk…as soon as she was able to stand up without getting dizzy. Ah, hell with it, she was getting up anyway – as long as she moved at a snail's pace, she felt fine.

The framed artwork went onto her desk, along with the photos of sleeping Tommy and running Tommy. That last photo, of her much younger self – that went on the nightstand.

"No one can ever know about that," she muttered, pushing the wrapping paper off her bed and putting the letter away.

"Are you talking to yourself? First sign of madness, they say." She glowered to the best of her ability at Sheppard, who had opened her door and poked his head in.

"What the hell are you doing here, flyboy?" she inquired hoarsely.

"Came to check on you. Cold any better?"

As a reply, she scowled and flung an empty tissue box at his head.

"Ow. I guess not. Hey, I think they've got soup in the mess today. Want some?"

"If you bring me a bowl of soup, I might tell you the story behind this picture," she said, indicating the one on the nightstand.

"I'll be back in a minute, and you can tell me all the potentially embarrassing stories you want."

"Soup, Sheppard! Now!" He withdrew, and she curled up in her bed and waited.

When John returned with the soup, she was already fast asleep. On the back of the letter from her sister, she'd scribbled a note.

_The picture on the nightstand was taken on the afternoon my daddy slipped me some red wine when my mama wasn't home. He loved to mess with all of us, and I don't guess I blame him – we girls outnumbered him four to one. Anyway, the incident in that photo occurred about six hours before my first hangover; I passed out on the kitchen floor. If you tell anyone about it, I'll kill you._

John just grinned to himself, gently tugged the covers to her chin, and quietly left her room. He'd tease her about it later, when she was feeling better (and not armed with small cardboard boxes with very pointy corners).

* * *

**A/N**: I wrote this in one sitting. I think it's my favorite so far, mostly because Lily's father is based loosely on my own grandfather (who was extremely mischievous – and he, too, was outnumbered 4-to-1 by my Gran, mother and aunts). This is for the greatest prankster I ever had the privilege to know.


	5. Lily, Alone

_Takes place in the alternate timeline of 'The Last Man'._

* * *

The day John steps through the Stargate and into the future, Lily's in the plant room tending quietly to some new additions. When Rodney – _Rodney,_ who after all this time still calls her 'Scarlett O'Hara' – appears in the doorway and uses her real name, she knows something's very, very wrong.

"What do you mean, he's in the future?" She's too shocked to form an intelligent question. Rodney doesn't seem to notice. He mentions any one of a dozen things that could send John Sheppard forty-eight thousand years away, but she understands only that her friend is gone.

When Teyla is found, Lily cries alone. Everyone else is too busy with their own sorrow to pay her any mind.

When Ronon and Sam die, she sheds no tears. Warriors should die in battle, it's only right – and they wouldn't want her to weep.

When Jennifer and Rodney decide to leave, she doesn't say a word to either of them; she chooses instead to follow them back to Earth.

A year later, now married to James Lassiter and with a newborn baby in her arms, she receives a phone call from an old friend.

"You probably don't remember me…" and it's Rodney McKay, and all the things she'd wanted to forget come rushing right back to her.

"Well, of course I remember you, Rodney!"

"Right. Uh…how are you, Lily?" She tells him – tells him she named her daughter for Samantha Carter, hopes he'll understand.

A few minutes later, she remembers her manners and asks how he's doing, how Jennifer is.

There's a long pause, in which her suspicions knot up her stomach, and then, "She died a couple of months ago." And the world seems to get just a little worse, a little darker – and she can't cry.

All her tears dried up when they found Teyla, and she's just been existing since then. What she has – her marriage, her daughter – has not made her truly happy. How can she be, when the only man she's ever loved is forty-eight thousand damned years in the future?

Yes, she realizes suddenly – in that instant before she finds the words to respond to Rodney – that she loves John Sheppard.

**Dammit, Sheppard, I love you** – she wishes she'd said it before, and doesn't realize she's said it aloud until Rodney replies.

"We all do. Did. Not – not the way you do, obviously, but we…" And she knows it's true, is more certain of that than of all else.

After a moment, "I'm sorry, Rodney. I…I've got to go." They say their goodbyes, and she hangs up. Jennifer Keller is gone, just like the rest before her. Lily doesn't know what to do.

He calls a few more times over the years, hurried conversations in the midst of all his calculations and work. She's raising a daughter, working nine-to-five – trying to be _normal,_ but they both know it's a lost cause. Neither of them will ever be 'normal' again, and barely know what that is.

Sixteen years after Atlantis, he calls her house for the last time. Samantha, the wrong Samantha with her mother's dark hair, answers.

"Is Lily there?"

"Who is this?"

"Rodney McKay." And in her heart, the girl wants to hate him, wants to scream at him, wants to know _why_.

Because Lily took her own life, picked up her husband's gun and ended everything. Because in the note she left, all she said was '**McKay will understand**'.

When he hears this, McKay goes back to his past-altering plans. She's the last in a half-dozen or more he needs to save, and he wonders when she became his friend. When they were on Atlantis, she was Jennifer's friend, John's friend – not his.

--

_"What about Lily?" Sheppard asked the hologram, almost afraid to hear the answer. He didn't want to hear that she ended up like the others, dead too soon, but he'd already asked the question._

_"She tried for a normal life, and managed it for several years. Married, had one daughter, named her Samantha. We spoke a few times, but the last time I called…she was already dead," the hologram told him, and Sheppard's expression flickered._

_"Sixteen years, she had a decent life, but Pegasus never really let her go. Once or twice, she sounded so hopeless…but she was strong, probably stronger than the rest of us combined – right up until that day."_

_Suicide. Jesus. Sheppard didn't want to think about it, that pretty little scientist who fought down the memories of Pegasus for so long, only to lose in the end._

_"She loved you, you know." With that last, they reached the stasis room._

--

Twelve days after disappearing, John Sheppard returned through the Stargate to the right time. Lily, who had avoided everyone for a dozen days, was just leaving her room when he showed up – without a word, he kissed her. It was over as soon as it had started, and she blinked up at the vaguely triumphant look in his eyes.

"How is it that you always know, John?" she whispered, feeling the tears building in her eyes. He didn't respond, just wrapped his arms around her and kissed the top of her head. There were things to be done – a medical exam to suffer through, a friend and her baby to save…but there was also this moment, the warmth of a good woman. It would just have to be enough for now.

* * *

**A/N:** All things must come to an end, even this. I don't know if there'll be a sequel – actually, anyone who wants to write their own has my permission. Make her go on new adventures, throw more Kleenex boxes, I don't care. Just be nice to her, please? Oh, and no one is allowed to ask why this is so shippy - mostly because I have no idea.


End file.
